GLM on abundance_pres

Calculate some info per sample

#calculate the Shannon-Wiener diversity (with diversity function from vegan package) for all species
df.sample_data$diversity <- apply(df.sample_data[df.species_all$colname], MARGIN=1, diversity)
#calculate the Shannon-Wiener diversity (with diversity function from vegan package) for nursery species
df.sample_data$nursery_diversity <- apply(df.sample_data[nursery_species$colname], MARGIN=1, diversity)

#calculate number of species for all species by summing the presence/absence columns for those species
df.sample_data$num_species <- apply(df.sample_data[c(df.species_all$colname_pres)],MARGIN=1,sum)
#calculate number of species for nursery species by summing the presence/absence columns for those species
df.sample_data$num_nursery_species <- apply(df.sample_data[c(nursery_species$colname_pres)],MARGIN=1,sum)

#calculate number of fish
df.sample_data$num_fish <- apply(df.sample_data[c(df.species_all$colname)],MARGIN=1,sum)
#calculate number of nursery fish
df.sample_data$num_nursery_fish <- apply(df.sample_data[c(nursery_species$colname)],MARGIN=1,sum)

df.sample_data <- merge(x=df.sample_data, y=df.sites, by.x="location", by.y="name", all.x=TRUE)

Nursery species

nursery_columns <- c(c("location","depth","transect","date","nursery_diversity","num_nursery_species","num_nursery_fish"),nursery_species$colname, nursery_species$colname_pres) #columns for nursery species analysis
df.nursery_sample_data <- df.sample_data[nursery_columns] # subset of the data with only the nursery species

GLM family=Poisson on abundance_pres

Independent variables: size_seagrass, distance_seagrass, size_mangroves, distance_mangroves, mpa, depth, north

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459547"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"

## Warning: glm.fit: algorithm did not converge

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028389"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$north"
## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"

## Warning: glm.fit: algorithm did not converge

## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
1	abudefduf_sexfasciatus	n$distance_seagrass	0.0475774
2	abudefduf_sexfasciatus	n$size_mangroves	0.0485260
21	abudefduf_vaigiensis	n$distance_seagrass	0.0007579
3	abudefduf_vaigiensis	n$size_seagrass	0.0024052
4	abudefduf_vaigiensis	n$size_mangroves	0.0007376
5	abudefduf_vaigiensis	n$distance_mangroves	0.0012850
6	abudefduf_vaigiensis	n$mpanon-mpa	0.0011287
7	abudefduf_vaigiensis	n$northsouth	0.0008274
8	abudefduf_vaigiensis	n\(distance_seagrass:n\)size_seagrass	0.0011290
9	abudefduf_vaigiensis	n\(distance_seagrass:n\)depth10m	0.0000186
10	abudefduf_vaigiensis	n\(size_seagrass:n\)depth10m	0.0016766
12	cheilio_inermis	n$depth10m	0.0057399
22	cheilodipterus_quinquelineatus	n$distance_seagrass	0.0002778
31	cheilodipterus_quinquelineatus	n$size_seagrass	0.0000000
41	cheilodipterus_quinquelineatus	n$size_mangroves	0.0003234
51	cheilodipterus_quinquelineatus	n$distance_mangroves	0.0000383
61	cheilodipterus_quinquelineatus	n$mpanon-mpa	0.0020950
71	cheilodipterus_quinquelineatus	n$northsouth	0.0000726
81	cheilodipterus_quinquelineatus	n\(size_seagrass:n\)depth10m	0.0000000
91	cheilodipterus_quinquelineatus	n\(distance_seagrass:n\)size_seagrass:n$depth10m	0.0009730
211	mulloidichthys_flavolineatus	n$distance_mangroves	0.0001437
221	mulloidichthys_flavolineatus	n$mpanon-mpa	0.0021100
23	parupeneus_barberinoides	n$distance_seagrass	0.0002228
24	scolopsis_ciliata	n$depth10m	0.0078945
25	scolopsis_ciliata	n\(distance_seagrass:n\)depth10m	0.0001718

log(size_seagrass)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459547"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC fistularia_commersonii :  203.808555954373"

## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC halichoeres_hortulanus :  621.430719922767"

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028388"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$north"
## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
2	abudefduf_sexfasciatus	n$size_mangroves	0.0232130
3	abudefduf_sexfasciatus	n$distance_mangroves	0.0266834
4	abudefduf_sexfasciatus	n$mpanon-mpa	0.0085069
5	abudefduf_sexfasciatus	n$northsouth	0.0343237
21	abudefduf_vaigiensis	n$distance_seagrass	0.0000299
31	abudefduf_vaigiensis	n$size_mangroves	0.0010257
41	abudefduf_vaigiensis	n$distance_mangroves	0.0019656
51	abudefduf_vaigiensis	n$mpanon-mpa	0.0011233
6	abudefduf_vaigiensis	n$depth10m	0.0002026
7	abudefduf_vaigiensis	n$northsouth	0.0010132
8	abudefduf_vaigiensis	n\(distance_seagrass:log(n\)size_seagrass)	0.0004283
9	abudefduf_vaigiensis	n\(distance_seagrass:n\)depth10m	0.0000013
10	abudefduf_vaigiensis	log(n\(size_seagrass):n\)depth10m	0.0016766
14	cheilio_inermis	n$depth10m	0.0057399
22	cheilodipterus_quinquelineatus	log(n$size_seagrass)	0.0000000
32	cheilodipterus_quinquelineatus	n$size_mangroves	0.0000002
42	cheilodipterus_quinquelineatus	n$distance_mangroves	0.0000000
52	cheilodipterus_quinquelineatus	n$mpanon-mpa	0.0000020
61	cheilodipterus_quinquelineatus	n$northsouth	0.0000002
71	cheilodipterus_quinquelineatus	n\(distance_seagrass:log(n\)size_seagrass)	0.0076134
81	cheilodipterus_quinquelineatus	n\(distance_seagrass:n\)depth10m	0.0067477
91	cheilodipterus_quinquelineatus	log(n\(size_seagrass):n\)depth10m	0.0000000
101	cheilodipterus_quinquelineatus	n\(distance_mangroves:n\)depth10m	0.0008222
11	cheilodipterus_quinquelineatus	n\(distance_seagrass:log(n\)size_seagrass):n$depth10m	0.0000338
25	fistularia_commersonii	log(n$size_seagrass)	0.0416231
26	fistularia_commersonii	n$distance_mangroves	0.0152579
27	fistularia_commersonii	n$mpanon-mpa	0.0109622
28	fistularia_commersonii	n\(distance_seagrass:n\)size_mangroves	0.0378217
23	halichoeres_hortulanus	n$distance_seagrass	0.0038113
33	halichoeres_hortulanus	log(n$size_seagrass)	0.0138281
43	halichoeres_hortulanus	n$size_mangroves	0.0099475
53	halichoeres_hortulanus	n$distance_mangroves	0.0103440
62	halichoeres_hortulanus	n$mpanon-mpa	0.0317664
72	halichoeres_hortulanus	n$northsouth	0.0109432
82	halichoeres_hortulanus	n\(distance_seagrass:n\)size_mangroves	0.0078294
36	mulloidichthys_flavolineatus	n$distance_seagrass	0.0170298
37	mulloidichthys_flavolineatus	n$distance_mangroves	0.0023050
38	mulloidichthys_flavolineatus	n$mpanon-mpa	0.0002856
39	parupeneus_barberinoides	n$distance_seagrass	0.0001312
40	scolopsis_ciliata	n$depth10m	0.0207127
411	scolopsis_ciliata	n\(distance_seagrass:n\)depth10m	0.0084546

log(distance_seagrass)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459546"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033752"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC halichoeres_hortulanus :  621.430719922767"

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028388"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinus :  633.195660521307"

## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$north"
## [1] "AIC lutjanus_fulviflamma :  37.6524153062094"

## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_bilineata :  843.933588478539"

## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * n$distance_mangroves * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
1	abudefduf_sexfasciatus	n$size_seagrass	0.0411274
2	abudefduf_vaigiensis	log(n$distance_seagrass)	0.0002140
3	abudefduf_vaigiensis	n$size_seagrass	0.0014448
4	abudefduf_vaigiensis	n$size_mangroves	0.0001557
5	abudefduf_vaigiensis	n$distance_mangroves	0.0021998
6	abudefduf_vaigiensis	n$mpanon-mpa	0.0013878
7	abudefduf_vaigiensis	n$depth10m	0.0000014
8	abudefduf_vaigiensis	n$northsouth	0.0023314
9	abudefduf_vaigiensis	log(n\(distance_seagrass):n\)size_seagrass	0.0012287
10	abudefduf_vaigiensis	log(n\(distance_seagrass):n\)depth10m	0.0000186
11	abudefduf_vaigiensis	n\(size_seagrass:n\)depth10m	0.0016766
12	cheilio_inermis	n$depth10m	0.0057399
13	cheilodipterus_quinquelineatus	log(n$distance_seagrass)	0.0008500
14	cheilodipterus_quinquelineatus	n$size_seagrass	0.0000151
15	cheilodipterus_quinquelineatus	n$size_mangroves	0.0017885
16	cheilodipterus_quinquelineatus	n$distance_mangroves	0.0003449
17	cheilodipterus_quinquelineatus	n$northsouth	0.0030186
18	cheilodipterus_quinquelineatus	log(n\(distance_seagrass):n\)size_seagrass	0.0042162
19	cheilodipterus_quinquelineatus	n\(size_seagrass:n\)depth10m	0.0034369
20	cheilodipterus_quinquelineatus	n\(size_mangroves:n\)depth10m	0.0137646
21	cheilodipterus_quinquelineatus	log(n\(distance_seagrass):n\)size_seagrass:n$depth10m	0.0097216
22	halichoeres_hortulanus	log(n$distance_seagrass)	0.0319946
31	halichoeres_hortulanus	n$size_mangroves	0.0079199
41	halichoeres_hortulanus	n$mpanon-mpa	0.0009165
51	halichoeres_hortulanus	n$northsouth	0.0003591
61	halichoeres_hortulanus	log(n\(distance_seagrass):n\)size_seagrass	0.0322807
71	halichoeres_hortulanus	log(n\(distance_seagrass):n\)size_mangroves	0.0083371
28	mulloidichthys_flavolineatus	log(n$distance_seagrass)	0.0245036
29	mulloidichthys_flavolineatus	n$distance_mangroves	0.0074226
30	mulloidichthys_flavolineatus	n$mpanon-mpa	0.0150556
23	parupeneus_barberinus	log(n$distance_seagrass)	0.0206391
32	parupeneus_barberinus	n$size_seagrass	0.0446283
42	parupeneus_barberinus	n$distance_mangroves	0.0189358
52	parupeneus_barberinus	n$northsouth	0.0471892
24	lutjanus_fulviflamma	n$size_seagrass	0.0487377
36	parupeneus_barberinoides	log(n$distance_seagrass)	0.0001737
37	scolopsis_bilineata	n\(distance_mangroves:n\)depth10m	0.0291154
38	scolopsis_ciliata	n$depth10m	0.0001206
39	scolopsis_ciliata	log(n\(distance_seagrass):n\)depth10m	0.0001718

log(size_mangroves)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459547"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"

## Warning: glm.fit: algorithm did not converge

## [1] "AIC halichoeres_hortulanus :  623.511082015147"

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028388"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$north"
## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"

## Warning: glm.fit: algorithm did not converge

## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
2	abudefduf_sexfasciatus	n$distance_seagrass	0.0475204
3	abudefduf_sexfasciatus	log(n$size_mangroves)	0.0485260
21	abudefduf_vaigiensis	n$distance_seagrass	0.0007519
31	abudefduf_vaigiensis	log(n$size_mangroves)	0.0007376
4	abudefduf_vaigiensis	n$distance_mangroves	0.0010258
5	abudefduf_vaigiensis	n$mpanon-mpa	0.0009591
6	abudefduf_vaigiensis	n$northsouth	0.0007727
7	abudefduf_vaigiensis	n\(distance_seagrass:n\)size_seagrass	0.0009839
8	abudefduf_vaigiensis	n\(distance_seagrass:n\)depth10m	0.0000186
9	abudefduf_vaigiensis	n\(size_seagrass:n\)depth10m	0.0016766
11	cheilio_inermis	n$depth10m	0.0057399
22	cheilodipterus_quinquelineatus	n$distance_seagrass	0.0002754
32	cheilodipterus_quinquelineatus	n$size_seagrass	0.0152336
41	cheilodipterus_quinquelineatus	log(n$size_mangroves)	0.0003234
51	cheilodipterus_quinquelineatus	n$distance_mangroves	0.0000564
61	cheilodipterus_quinquelineatus	n$mpanon-mpa	0.0027557
71	cheilodipterus_quinquelineatus	n$northsouth	0.0001337
81	cheilodipterus_quinquelineatus	n\(distance_seagrass:n\)size_seagrass	0.0468577
91	cheilodipterus_quinquelineatus	n\(size_seagrass:n\)depth10m	0.0000000
10	cheilodipterus_quinquelineatus	n\(distance_seagrass:n\)size_seagrass:n$depth10m	0.0015202
23	halichoeres_hortulanus	n$distance_seagrass	0.0015355
33	halichoeres_hortulanus	n$size_seagrass	0.0020170
42	halichoeres_hortulanus	log(n$size_mangroves)	0.0016483
52	halichoeres_hortulanus	n$distance_mangroves	0.0020266
62	halichoeres_hortulanus	n$mpanon-mpa	0.0022771
72	halichoeres_hortulanus	n$northsouth	0.0017666
82	halichoeres_hortulanus	n\(distance_seagrass:n\)size_seagrass	0.0016340
92	halichoeres_hortulanus	n\(distance_seagrass:log(n\)size_mangroves)	0.0015467
29	mulloidichthys_flavolineatus	n$distance_mangroves	0.0001436
30	mulloidichthys_flavolineatus	n$mpanon-mpa	0.0025719
311	parupeneus_barberinoides	n$distance_seagrass	0.0010270
321	scolopsis_ciliata	n$depth10m	0.0078945
331	scolopsis_ciliata	n\(distance_seagrass:n\)depth10m	0.0001718

log(distance_mangroves)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459546"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC halichoeres_hortulanus :  621.430719922767"

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC lutjanus_gibbus :  54.9453245875361"

## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028388"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinus :  633.195660521307"

## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$north"
## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_bilineata :  843.933588478539"

## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$distance_mangroves) * n$size_mangroves * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

species	coefficient	pvalue
abudefduf_sexfasciatus	n\(distance_seagrass:n\)size_seagrass	0.0072912
abudefduf_vaigiensis	n$distance_seagrass	0.0004432
abudefduf_vaigiensis	n$size_seagrass	0.0010183
abudefduf_vaigiensis	log(n$distance_mangroves)	0.0012850
abudefduf_vaigiensis	n$size_mangroves	0.0004442
abudefduf_vaigiensis	n$mpanon-mpa	0.0010418
abudefduf_vaigiensis	n$northsouth	0.0006305
abudefduf_vaigiensis	n\(distance_seagrass:n\)size_seagrass	0.0008741
abudefduf_vaigiensis	n\(distance_seagrass:n\)depth10m	0.0000186
abudefduf_vaigiensis	n\(size_seagrass:n\)depth10m	0.0016766
cheilio_inermis	n$depth10m	0.0057399
cheilodipterus_quinquelineatus	n$distance_seagrass	0.0000560
cheilodipterus_quinquelineatus	n$size_seagrass	0.0000000
cheilodipterus_quinquelineatus	log(n$distance_mangroves)	0.0000383
cheilodipterus_quinquelineatus	n$size_mangroves	0.0000797
cheilodipterus_quinquelineatus	n$mpanon-mpa	0.0044880
cheilodipterus_quinquelineatus	n$depth10m	0.0471287
cheilodipterus_quinquelineatus	n$northsouth	0.0000206
cheilodipterus_quinquelineatus	n\(distance_seagrass:n\)size_seagrass	0.0000000
cheilodipterus_quinquelineatus	n\(mpanon-mpa:n\)depth10m	0.0254092
cheilodipterus_quinquelineatus	n\(distance_seagrass:n\)size_seagrass:n$depth10m	0.0006448
halichoeres_hortulanus	n$distance_seagrass	0.0033563
halichoeres_hortulanus	log(n$distance_mangroves)	0.0188338
halichoeres_hortulanus	n$mpanon-mpa	0.0015347
halichoeres_hortulanus	n\(distance_seagrass:log(n\)distance_mangroves)	0.0030464
lutjanus_gibbus	n$size_seagrass	0.0001858
mulloidichthys_flavolineatus	n$distance_seagrass	0.0001114
mulloidichthys_flavolineatus	n$size_seagrass	0.0003739
mulloidichthys_flavolineatus	log(n$distance_mangroves)	0.0001437
mulloidichthys_flavolineatus	n$mpanon-mpa	0.0002624
parupeneus_barberinus	n$size_seagrass	0.0289434
parupeneus_barberinus	n$size_mangroves	0.0311172
parupeneus_barberinus	n$northsouth	0.0474017
parupeneus_barberinus	n\(distance_seagrass:n\)size_seagrass	0.0165494
scolopsis_bilineata	n\(size_seagrass:n\)depth10m	0.0134165
scolopsis_ciliata	n$depth10m	0.0078945
scolopsis_ciliata	n\(distance_seagrass:n\)depth10m	0.0001718

log(size_seagrass) & log(distance_seagrass)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459547"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC halichoeres_hortulanus :  621.430719922767"

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028389"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinus :  633.195660521307"

## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$north"
## [1] "AIC lutjanus_fulviflamma :  37.6524153062094"

## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * n$size_mangroves * n$distance_mangroves * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
2	abudefduf_sexfasciatus	log(n$size_seagrass)	0.0314838
3	abudefduf_sexfasciatus	n$size_mangroves	0.0221253
4	abudefduf_sexfasciatus	n$distance_mangroves	0.0360156
5	abudefduf_sexfasciatus	n$mpanon-mpa	0.0293558
6	abudefduf_sexfasciatus	log(n\(distance_seagrass):log(n\)size_seagrass)	0.0342116
21	abudefduf_vaigiensis	log(n$distance_seagrass)	0.0039717
31	abudefduf_vaigiensis	log(n$size_seagrass)	0.0014468
41	abudefduf_vaigiensis	n$size_mangroves	0.0009734
51	abudefduf_vaigiensis	n$distance_mangroves	0.0010066
61	abudefduf_vaigiensis	n$mpanon-mpa	0.0010933
7	abudefduf_vaigiensis	n$depth10m	0.0000008
8	abudefduf_vaigiensis	n$northsouth	0.0010383
9	abudefduf_vaigiensis	log(n\(distance_seagrass):log(n\)size_seagrass)	0.0011791
10	abudefduf_vaigiensis	log(n\(distance_seagrass):n\)depth10m	0.0000013
11	abudefduf_vaigiensis	log(n\(size_seagrass):n\)depth10m	0.0016766
16	cheilio_inermis	n$depth10m	0.0057399
17	cheilodipterus_quinquelineatus	log(n$distance_seagrass)	0.0218050
18	cheilodipterus_quinquelineatus	log(n$size_seagrass)	0.0000000
19	cheilodipterus_quinquelineatus	n$size_mangroves	0.0000013
20	cheilodipterus_quinquelineatus	n$distance_mangroves	0.0000000
211	cheilodipterus_quinquelineatus	n$mpanon-mpa	0.0000136
22	cheilodipterus_quinquelineatus	log(n\(distance_seagrass):log(n\)size_seagrass)	0.0000017
23	cheilodipterus_quinquelineatus	log(n\(distance_seagrass):n\)depth10m	0.0134930
24	cheilodipterus_quinquelineatus	log(n\(size_seagrass):n\)depth10m	0.0036135
25	cheilodipterus_quinquelineatus	log(n\(distance_seagrass):log(n\)size_seagrass):n$depth10m	0.0028510
26	halichoeres_hortulanus	log(n$distance_seagrass)	0.0082914
32	halichoeres_hortulanus	log(n$size_seagrass)	0.0378139
42	halichoeres_hortulanus	n$size_mangroves	0.0042414
52	halichoeres_hortulanus	n$distance_mangroves	0.0161226
62	halichoeres_hortulanus	n$mpanon-mpa	0.0015648
71	halichoeres_hortulanus	n$northsouth	0.0021504
81	halichoeres_hortulanus	log(n\(distance_seagrass):n\)size_mangroves	0.0044979
27	mulloidichthys_flavolineatus	log(n$distance_seagrass)	0.0170723
33	mulloidichthys_flavolineatus	n$size_mangroves	0.0051032
43	mulloidichthys_flavolineatus	n$distance_mangroves	0.0146713
53	mulloidichthys_flavolineatus	n$mpanon-mpa	0.0134271
63	mulloidichthys_flavolineatus	n$northsouth	0.0049402
38	parupeneus_barberinus	log(n$size_seagrass)	0.0269771
39	parupeneus_barberinus	n$distance_mangroves	0.0481660
40	parupeneus_barberinus	log(n\(distance_seagrass):log(n\)size_seagrass)	0.0130958
411	lutjanus_fulviflamma	log(n$size_seagrass)	0.0487377
421	parupeneus_barberinoides	log(n$distance_seagrass)	0.0001365
431	scolopsis_ciliata	n$depth10m	0.0005535
44	scolopsis_ciliata	log(n\(distance_seagrass):n\)depth10m	0.0084546

log(size_seagrass) & log(size_mangroves)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459547"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC fistularia_commersonii :  203.808555954373"

## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC halichoeres_hortulanus :  621.430719922767"

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028388"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$north"
## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * n$distance_mangroves * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
2	abudefduf_sexfasciatus	log(n$size_mangroves)	0.0232130
3	abudefduf_sexfasciatus	n$mpanon-mpa	0.0082701
4	abudefduf_sexfasciatus	n$northsouth	0.0306714
21	abudefduf_vaigiensis	n$distance_seagrass	0.0000256
31	abudefduf_vaigiensis	log(n$size_seagrass)	0.0363995
41	abudefduf_vaigiensis	log(n$size_mangroves)	0.0010257
5	abudefduf_vaigiensis	n$distance_mangroves	0.0020795
6	abudefduf_vaigiensis	n$mpanon-mpa	0.0012202
7	abudefduf_vaigiensis	n$depth10m	0.0002026
8	abudefduf_vaigiensis	n$northsouth	0.0010107
9	abudefduf_vaigiensis	n\(distance_seagrass:log(n\)size_seagrass)	0.0001835
10	abudefduf_vaigiensis	n\(distance_seagrass:n\)depth10m	0.0000013
11	abudefduf_vaigiensis	log(n\(size_seagrass):n\)depth10m	0.0016766
14	cheilio_inermis	n$depth10m	0.0057399
22	cheilodipterus_quinquelineatus	log(n$size_mangroves)	0.0000002
32	cheilodipterus_quinquelineatus	n$distance_mangroves	0.0000000
42	cheilodipterus_quinquelineatus	n$mpanon-mpa	0.0000011
51	cheilodipterus_quinquelineatus	n$northsouth	0.0000002
61	cheilodipterus_quinquelineatus	n\(distance_seagrass:log(n\)size_seagrass)	0.0260604
71	cheilodipterus_quinquelineatus	n\(distance_seagrass:n\)depth10m	0.0025727
81	cheilodipterus_quinquelineatus	log(n\(size_seagrass):n\)depth10m	0.0000002
91	cheilodipterus_quinquelineatus	n\(distance_mangroves:n\)depth10m	0.0001081
101	cheilodipterus_quinquelineatus	n\(distance_seagrass:log(n\)size_seagrass):n$depth10m	0.0000341
24	fistularia_commersonii	n$distance_seagrass	0.0328563
25	fistularia_commersonii	log(n$size_seagrass)	0.0406923
26	fistularia_commersonii	n$distance_mangroves	0.0146087
27	fistularia_commersonii	n$mpanon-mpa	0.0107055
28	fistularia_commersonii	n$northsouth	0.0486197
29	fistularia_commersonii	n\(distance_seagrass:log(n\)size_mangroves)	0.0259648
23	halichoeres_hortulanus	n$distance_seagrass	0.0059966
33	halichoeres_hortulanus	log(n$size_seagrass)	0.0129899
43	halichoeres_hortulanus	log(n$size_mangroves)	0.0089956
52	halichoeres_hortulanus	n$distance_mangroves	0.0099240
62	halichoeres_hortulanus	n$mpanon-mpa	0.0278040
72	halichoeres_hortulanus	n$northsouth	0.0105687
82	halichoeres_hortulanus	n\(distance_seagrass:log(n\)size_mangroves)	0.0066500
37	mulloidichthys_flavolineatus	n$distance_seagrass	0.0166240
38	mulloidichthys_flavolineatus	n$distance_mangroves	0.0020101
39	mulloidichthys_flavolineatus	n$mpanon-mpa	0.0002878
40	parupeneus_barberinoides	n$distance_seagrass	0.0001620
411	scolopsis_ciliata	n$depth10m	0.0207127
421	scolopsis_ciliata	n\(distance_seagrass:n\)depth10m	0.0084546

log(size_seagrass) & log(distance_mangroves)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459547"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC fistularia_commersonii :  203.808555954373"

## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC halichoeres_hortulanus :  621.430719922767"

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028388"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinus :  633.195660521307"

## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$north"
## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_bilineata :  843.933588478539"

## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * n$size_mangroves * log(n$distance_mangroves) * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
1	abudefduf_sexfasciatus	log(n$size_seagrass)	0.0179729
2	abudefduf_sexfasciatus	log(n$distance_mangroves)	0.0266833
21	abudefduf_vaigiensis	n$distance_seagrass	0.0000034
3	abudefduf_vaigiensis	log(n$size_seagrass)	0.0002633
4	abudefduf_vaigiensis	n$size_mangroves	0.0009244
5	abudefduf_vaigiensis	log(n$distance_mangroves)	0.0019656
6	abudefduf_vaigiensis	n$depth10m	0.0002026
7	abudefduf_vaigiensis	n$northsouth	0.0007809
8	abudefduf_vaigiensis	n\(distance_seagrass:log(n\)size_seagrass)	0.0002590
9	abudefduf_vaigiensis	n\(distance_seagrass:n\)depth10m	0.0000013
10	abudefduf_vaigiensis	log(n\(size_seagrass):n\)depth10m	0.0016766
12	cheilio_inermis	n$depth10m	0.0057399
13	cheilodipterus_quinquelineatus	n$distance_seagrass	0.0004843
14	cheilodipterus_quinquelineatus	log(n$size_seagrass)	0.0000000
15	cheilodipterus_quinquelineatus	n$size_mangroves	0.0000000
16	cheilodipterus_quinquelineatus	log(n$distance_mangroves)	0.0000000
17	cheilodipterus_quinquelineatus	n$mpanon-mpa	0.0000000
18	cheilodipterus_quinquelineatus	n$depth10m	0.0033293
19	cheilodipterus_quinquelineatus	n$northsouth	0.0000000
20	cheilodipterus_quinquelineatus	n\(distance_seagrass:log(n\)size_seagrass)	0.0000000
211	cheilodipterus_quinquelineatus	log(n\(size_seagrass):n\)depth10m	0.0054286
22	cheilodipterus_quinquelineatus	n\(size_mangroves:n\)depth10m	0.0000155
23	cheilodipterus_quinquelineatus	log(n\(distance_mangroves):n\)depth10m	0.0008221
24	cheilodipterus_quinquelineatus	n\(mpanon-mpa:n\)depth10m	0.0000943
25	cheilodipterus_quinquelineatus	n\(depth10m:n\)northsouth	0.0000343
26	fistularia_commersonii	log(n$size_seagrass)	0.0411079
27	fistularia_commersonii	log(n$distance_mangroves)	0.0152579
28	halichoeres_hortulanus	n$distance_seagrass	0.0003595
29	halichoeres_hortulanus	log(n$size_seagrass)	0.0093301
30	halichoeres_hortulanus	n$size_mangroves	0.0323553
31	halichoeres_hortulanus	log(n$distance_mangroves)	0.0103440
32	halichoeres_hortulanus	n$mpanon-mpa	0.0013058
33	halichoeres_hortulanus	n\(distance_seagrass:log(n\)size_seagrass)	0.0042878
34	mulloidichthys_flavolineatus	n$distance_seagrass	0.0078900
35	mulloidichthys_flavolineatus	log(n$size_seagrass)	0.0005353
36	mulloidichthys_flavolineatus	log(n$distance_mangroves)	0.0023050
37	mulloidichthys_flavolineatus	n$mpanon-mpa	0.0226706
210	parupeneus_barberinus	n\(distance_seagrass:n\)size_mangroves	0.0463536
39	parupeneus_barberinoides	n$distance_seagrass	0.0001312
40	scolopsis_bilineata	n$depth10m	0.0332285
41	scolopsis_bilineata	n\(distance_seagrass:n\)size_mangroves:n$depth10m	0.0234958
42	scolopsis_ciliata	n$depth10m	0.0207127
43	scolopsis_ciliata	n\(distance_seagrass:n\)depth10m	0.0084546

log(size_seagrass), log(distance_mangroves) & log(size_mangroves)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459547"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC fistularia_commersonii :  203.808555954373"

## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC halichoeres_hortulanus :  621.430719922767"

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028388"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinus :  633.195660521307"

## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$north"
## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ n$distance_seagrass * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
1	abudefduf_sexfasciatus	log(n$size_seagrass)	0.0344264
2	abudefduf_vaigiensis	n$distance_seagrass	0.0000049
3	abudefduf_vaigiensis	log(n$size_seagrass)	0.0002024
4	abudefduf_vaigiensis	log(n$size_mangroves)	0.0009244
5	abudefduf_vaigiensis	log(n$distance_mangroves)	0.0020795
6	abudefduf_vaigiensis	n$mpanon-mpa	0.0115530
7	abudefduf_vaigiensis	n$depth10m	0.0002026
8	abudefduf_vaigiensis	n$northsouth	0.0007416
9	abudefduf_vaigiensis	n\(distance_seagrass:log(n\)size_seagrass)	0.0000672
10	abudefduf_vaigiensis	n\(distance_seagrass:n\)depth10m	0.0000013
11	abudefduf_vaigiensis	log(n\(size_seagrass):n\)depth10m	0.0016766
12	cheilio_inermis	n$depth10m	0.0057399
21	cheilodipterus_quinquelineatus	n$distance_seagrass	0.0000001
31	cheilodipterus_quinquelineatus	log(n$size_seagrass)	0.0000000
41	cheilodipterus_quinquelineatus	log(n$size_mangroves)	0.0000000
51	cheilodipterus_quinquelineatus	log(n$distance_mangroves)	0.0000000
61	cheilodipterus_quinquelineatus	n$mpanon-mpa	0.0000000
71	cheilodipterus_quinquelineatus	n$depth10m	0.0000137
81	cheilodipterus_quinquelineatus	n$northsouth	0.0000000
91	cheilodipterus_quinquelineatus	n\(distance_seagrass:log(n\)size_seagrass)	0.0000000
101	cheilodipterus_quinquelineatus	log(n\(size_seagrass):n\)depth10m	0.0011066
111	cheilodipterus_quinquelineatus	log(n\(size_mangroves):n\)depth10m	0.0000155
121	cheilodipterus_quinquelineatus	log(n\(distance_mangroves):n\)depth10m	0.0001081
13	cheilodipterus_quinquelineatus	n\(mpanon-mpa:n\)depth10m	0.0000085
14	cheilodipterus_quinquelineatus	n\(depth10m:n\)northsouth	0.0000190
15	cheilodipterus_quinquelineatus	n\(distance_seagrass:log(n\)size_seagrass):n$depth10m	0.0023942
27	fistularia_commersonii	log(n$distance_mangroves)	0.0146087
28	halichoeres_hortulanus	log(n$size_seagrass)	0.0093844
29	halichoeres_hortulanus	log(n$size_mangroves)	0.0327519
30	halichoeres_hortulanus	log(n$distance_mangroves)	0.0099240
311	halichoeres_hortulanus	n$mpanon-mpa	0.0013420
32	halichoeres_hortulanus	n\(distance_seagrass:log(n\)size_seagrass)	0.0035987
33	mulloidichthys_flavolineatus	n$distance_seagrass	0.0071981
34	mulloidichthys_flavolineatus	log(n$size_seagrass)	0.0006837
35	mulloidichthys_flavolineatus	log(n$distance_mangroves)	0.0020101
36	mulloidichthys_flavolineatus	n$mpanon-mpa	0.0219319
37	parupeneus_barberinus	n$northsouth	0.0467278
38	parupeneus_barberinoides	n$distance_seagrass	0.0001620
39	scolopsis_ciliata	n$depth10m	0.0207127
40	scolopsis_ciliata	n\(distance_seagrass:n\)depth10m	0.0084546

log(distance_seagrass) & log(distance_mangroves)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459547"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC halichoeres_hortulanus :  621.430719922767"

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028388"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinus :  633.195660521307"

## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$north"
## [1] "AIC lutjanus_fulviflamma :  37.6524153062094"

## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_bilineata :  843.933588478539"

## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * n$size_mangroves * log(n$distance_mangroves) * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
1	abudefduf_sexfasciatus	n$size_seagrass	0.0392477
2	abudefduf_sexfasciatus	n$size_mangroves	0.0497482
3	abudefduf_sexfasciatus	log(n\(distance_seagrass):n\)size_seagrass	0.0059002
21	abudefduf_vaigiensis	log(n$distance_seagrass)	0.0002270
31	abudefduf_vaigiensis	n$size_seagrass	0.0002630
4	abudefduf_vaigiensis	n$size_mangroves	0.0003707
5	abudefduf_vaigiensis	log(n$distance_mangroves)	0.0021998
6	abudefduf_vaigiensis	n$mpanon-mpa	0.0014699
7	abudefduf_vaigiensis	n$depth10m	0.0000014
8	abudefduf_vaigiensis	n$northsouth	0.0022516
9	abudefduf_vaigiensis	log(n\(distance_seagrass):n\)size_seagrass	0.0008789
10	abudefduf_vaigiensis	log(n\(distance_seagrass):n\)depth10m	0.0000186
11	abudefduf_vaigiensis	n\(size_seagrass:n\)depth10m	0.0016766
14	cheilio_inermis	n$depth10m	0.0057399
22	cheilodipterus_quinquelineatus	log(n$distance_seagrass)	0.0004298
32	cheilodipterus_quinquelineatus	n$size_seagrass	0.0000000
41	cheilodipterus_quinquelineatus	n$size_mangroves	0.0022527
51	cheilodipterus_quinquelineatus	log(n$distance_mangroves)	0.0003456
61	cheilodipterus_quinquelineatus	log(n\(distance_seagrass):n\)size_seagrass	0.0000000
71	cheilodipterus_quinquelineatus	n\(size_mangroves:n\)depth10m	0.0112231
81	cheilodipterus_quinquelineatus	n\(mpanon-mpa:n\)depth10m	0.0094656
91	cheilodipterus_quinquelineatus	log(n\(distance_seagrass):n\)size_seagrass:n$depth10m	0.0103284
23	halichoeres_hortulanus	log(n$distance_seagrass)	0.0288915
33	halichoeres_hortulanus	n$size_mangroves	0.0056661
42	halichoeres_hortulanus	n$mpanon-mpa	0.0012214
52	halichoeres_hortulanus	n$northsouth	0.0006473
62	halichoeres_hortulanus	log(n\(distance_seagrass):n\)size_mangroves	0.0065564
28	mulloidichthys_flavolineatus	log(n$distance_seagrass)	0.0007029
29	mulloidichthys_flavolineatus	log(n$distance_mangroves)	0.0074226
30	mulloidichthys_flavolineatus	n$mpanon-mpa	0.0011043
24	parupeneus_barberinus	log(n$distance_seagrass)	0.0088265
34	parupeneus_barberinus	n$size_seagrass	0.0047117
43	parupeneus_barberinus	n$size_mangroves	0.0218534
53	parupeneus_barberinus	log(n$distance_mangroves)	0.0189358
63	parupeneus_barberinus	n$northsouth	0.0061157
72	parupeneus_barberinus	log(n\(distance_seagrass):n\)size_seagrass	0.0042743
82	parupeneus_barberinus	log(n\(distance_seagrass):n\)size_mangroves	0.0182459
25	lutjanus_fulviflamma	n$size_seagrass	0.0487377
39	parupeneus_barberinoides	log(n$distance_seagrass)	0.0001737
40	scolopsis_bilineata	n$depth10m	0.0440425
411	scolopsis_bilineata	n\(size_seagrass:n\)depth10m	0.0121483
421	scolopsis_bilineata	log(n\(distance_mangroves):n\)depth10m	0.0291154
431	scolopsis_bilineata	log(n\(distance_seagrass):n\)size_seagrass:n$depth10m	0.0366272
44	scolopsis_ciliata	n$depth10m	0.0001206
45	scolopsis_ciliata	log(n\(distance_seagrass):n\)depth10m	0.0001718

log(distance_seagrass) & log(size_mangroves)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459547"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC halichoeres_hortulanus :  621.430719922767"

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028389"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinus :  633.195660521307"

## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$north"
## [1] "AIC lutjanus_fulviflamma :  37.6524153062094"

## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_bilineata :  843.933588478539"

## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * n$distance_mangroves * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
1	abudefduf_sexfasciatus	n$size_seagrass	0.0463933
2	abudefduf_vaigiensis	log(n$distance_seagrass)	0.0002138
3	abudefduf_vaigiensis	n$size_seagrass	0.0014430
4	abudefduf_vaigiensis	log(n$size_mangroves)	0.0001557
5	abudefduf_vaigiensis	n$distance_mangroves	0.0020967
6	abudefduf_vaigiensis	n$mpanon-mpa	0.0013417
7	abudefduf_vaigiensis	n$depth10m	0.0000014
8	abudefduf_vaigiensis	n$northsouth	0.0012362
9	abudefduf_vaigiensis	log(n\(distance_seagrass):n\)size_seagrass	0.0012096
10	abudefduf_vaigiensis	log(n\(distance_seagrass):n\)depth10m	0.0000186
11	abudefduf_vaigiensis	n\(size_seagrass:n\)depth10m	0.0016766
12	cheilio_inermis	n$depth10m	0.0057399
21	cheilodipterus_quinquelineatus	log(n$distance_seagrass)	0.0008526
31	cheilodipterus_quinquelineatus	n$size_seagrass	0.0000178
41	cheilodipterus_quinquelineatus	log(n$size_mangroves)	0.0017893
51	cheilodipterus_quinquelineatus	n$distance_mangroves	0.0003605
61	cheilodipterus_quinquelineatus	n$depth10m	0.0055779
71	cheilodipterus_quinquelineatus	n$northsouth	0.0000440
81	cheilodipterus_quinquelineatus	log(n\(distance_seagrass):n\)size_seagrass	0.0039681
91	cheilodipterus_quinquelineatus	n\(size_seagrass:n\)depth10m	0.0026726
101	cheilodipterus_quinquelineatus	log(n\(size_mangroves):n\)depth10m	0.0137667
111	cheilodipterus_quinquelineatus	log(n\(distance_seagrass):n\)size_seagrass:n$depth10m	0.0104406
22	halichoeres_hortulanus	log(n$distance_seagrass)	0.0094783
32	halichoeres_hortulanus	log(n$size_mangroves)	0.0078039
42	halichoeres_hortulanus	n$mpanon-mpa	0.0007428
52	halichoeres_hortulanus	n$northsouth	0.0002184
62	halichoeres_hortulanus	log(n\(distance_seagrass):n\)size_seagrass	0.0349378
72	halichoeres_hortulanus	log(n\(distance_seagrass):log(n\)size_mangroves)	0.0081729
29	mulloidichthys_flavolineatus	log(n$distance_seagrass)	0.0265570
30	mulloidichthys_flavolineatus	n$distance_mangroves	0.0090560
311	mulloidichthys_flavolineatus	n$mpanon-mpa	0.0171668
321	parupeneus_barberinus	n$size_seagrass	0.0413453
33	parupeneus_barberinus	n$distance_mangroves	0.0164943
23	lutjanus_fulviflamma	n$size_seagrass	0.0487377
35	parupeneus_barberinoides	log(n$distance_seagrass)	0.0002570
36	scolopsis_bilineata	n\(distance_mangroves:n\)depth10m	0.0260803
37	scolopsis_ciliata	n$depth10m	0.0001206
38	scolopsis_ciliata	log(n\(distance_seagrass):n\)depth10m	0.0001718

log(distance_mangroves) & log(size_mangroves)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459547"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"

## Warning: glm.fit: algorithm did not converge

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028388"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"

## Warning: glm.fit: algorithm did not converge

## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$north"
## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"

## Warning: glm.fit: algorithm did not converge

## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ n$distance_seagrass * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
1	abudefduf_sexfasciatus	n\(distance_seagrass:n\)size_seagrass	0.0072771
2	abudefduf_vaigiensis	n$distance_seagrass	0.0004432
3	abudefduf_vaigiensis	n$size_seagrass	0.0007703
4	abudefduf_vaigiensis	log(n$size_mangroves)	0.0004442
5	abudefduf_vaigiensis	log(n$distance_mangroves)	0.0010258
6	abudefduf_vaigiensis	n$mpanon-mpa	0.0008888
7	abudefduf_vaigiensis	n$northsouth	0.0005413
8	abudefduf_vaigiensis	n\(distance_seagrass:n\)size_seagrass	0.0008599
9	abudefduf_vaigiensis	n\(distance_seagrass:n\)depth10m	0.0000186
10	abudefduf_vaigiensis	n\(size_seagrass:n\)depth10m	0.0016766
11	cheilio_inermis	n$depth10m	0.0057399
21	cheilodipterus_quinquelineatus	n$distance_seagrass	0.0000543
31	cheilodipterus_quinquelineatus	n$size_seagrass	0.0000000
41	cheilodipterus_quinquelineatus	log(n$size_mangroves)	0.0000797
51	cheilodipterus_quinquelineatus	log(n$distance_mangroves)	0.0000564
61	cheilodipterus_quinquelineatus	n$mpanon-mpa	0.0057188
71	cheilodipterus_quinquelineatus	n$northsouth	0.0000348
81	cheilodipterus_quinquelineatus	n\(distance_seagrass:n\)size_seagrass	0.0000000
91	cheilodipterus_quinquelineatus	n\(size_seagrass:n\)depth10m	0.0115788
101	cheilodipterus_quinquelineatus	n\(mpanon-mpa:n\)depth10m	0.0249994
111	cheilodipterus_quinquelineatus	n\(distance_seagrass:n\)size_seagrass:n$depth10m	0.0006490
22	mulloidichthys_flavolineatus	n$distance_seagrass	0.0000959
23	mulloidichthys_flavolineatus	n$size_seagrass	0.0004580
24	mulloidichthys_flavolineatus	log(n$distance_mangroves)	0.0001436
25	mulloidichthys_flavolineatus	n$mpanon-mpa	0.0002494
26	parupeneus_barberinoides	n$distance_seagrass	0.0010270
27	scolopsis_ciliata	n$depth10m	0.0078945
28	scolopsis_ciliata	n\(distance_seagrass:n\)depth10m	0.0001718

log(distance_seagrass), log(distance_mangroves) & log(size_mangroves)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459547"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC halichoeres_hortulanus :  621.430719922767"

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028389"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinus :  633.195660521307"

## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$north"
## [1] "AIC lutjanus_fulviflamma :  37.6524153062094"

## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_bilineata :  843.933588478539"

## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * n$size_seagrass * log(n$size_mangroves) * log(n$distance_mangroves) * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
1	abudefduf_sexfasciatus	n$size_seagrass	0.0404488
2	abudefduf_sexfasciatus	log(n$size_mangroves)	0.0497482
3	abudefduf_sexfasciatus	log(n\(distance_seagrass):n\)size_seagrass	0.0058995
21	abudefduf_vaigiensis	log(n$distance_seagrass)	0.0002275
31	abudefduf_vaigiensis	n$size_seagrass	0.0003546
4	abudefduf_vaigiensis	log(n$size_mangroves)	0.0003707
5	abudefduf_vaigiensis	log(n$distance_mangroves)	0.0020967
6	abudefduf_vaigiensis	n$mpanon-mpa	0.0014231
7	abudefduf_vaigiensis	n$depth10m	0.0000014
8	abudefduf_vaigiensis	n$northsouth	0.0015942
9	abudefduf_vaigiensis	log(n\(distance_seagrass):n\)size_seagrass	0.0008776
10	abudefduf_vaigiensis	log(n\(distance_seagrass):n\)depth10m	0.0000186
11	abudefduf_vaigiensis	n\(size_seagrass:n\)depth10m	0.0016766
14	cheilio_inermis	n$depth10m	0.0057399
15	cheilodipterus_quinquelineatus	log(n$distance_seagrass)	0.0004282
16	cheilodipterus_quinquelineatus	n$size_seagrass	0.0000000
17	cheilodipterus_quinquelineatus	log(n$size_mangroves)	0.0022527
18	cheilodipterus_quinquelineatus	log(n$distance_mangroves)	0.0003605
19	cheilodipterus_quinquelineatus	n$depth10m	0.0043554
20	cheilodipterus_quinquelineatus	log(n\(distance_seagrass):n\)size_seagrass	0.0000000
211	cheilodipterus_quinquelineatus	log(n\(size_mangroves):n\)depth10m	0.0112231
22	cheilodipterus_quinquelineatus	n\(mpanon-mpa:n\)depth10m	0.0094756
23	cheilodipterus_quinquelineatus	log(n\(distance_seagrass):n\)size_seagrass:n$depth10m	0.0101167
24	halichoeres_hortulanus	log(n$distance_seagrass)	0.0073088
32	halichoeres_hortulanus	log(n$size_mangroves)	0.0048756
41	halichoeres_hortulanus	n$mpanon-mpa	0.0009862
51	halichoeres_hortulanus	n$northsouth	0.0002722
61	halichoeres_hortulanus	log(n\(distance_seagrass):log(n\)size_mangroves)	0.0060820
29	mulloidichthys_flavolineatus	log(n$distance_seagrass)	0.0005879
30	mulloidichthys_flavolineatus	log(n$distance_mangroves)	0.0090560
311	mulloidichthys_flavolineatus	n$mpanon-mpa	0.0011129
25	parupeneus_barberinus	log(n$distance_seagrass)	0.0166298
33	parupeneus_barberinus	n$size_seagrass	0.0038628
42	parupeneus_barberinus	log(n$size_mangroves)	0.0316462
52	parupeneus_barberinus	log(n$distance_mangroves)	0.0164943
62	parupeneus_barberinus	n$mpanon-mpa	0.0484746
71	parupeneus_barberinus	n$northsouth	0.0111891
81	parupeneus_barberinus	log(n\(distance_seagrass):n\)size_seagrass	0.0035053
91	parupeneus_barberinus	log(n\(distance_seagrass):log(n\)size_mangroves)	0.0197465
26	lutjanus_fulviflamma	n$size_seagrass	0.0487377
411	parupeneus_barberinoides	log(n$distance_seagrass)	0.0002570
421	scolopsis_bilineata	n\(size_seagrass:n\)depth10m	0.0083236
43	scolopsis_bilineata	log(n\(distance_mangroves):n\)depth10m	0.0260803
44	scolopsis_bilineata	log(n\(distance_seagrass):n\)size_seagrass:n$depth10m	0.0292520
45	scolopsis_ciliata	n$depth10m	0.0001206
46	scolopsis_ciliata	log(n\(distance_seagrass):n\)depth10m	0.0001718

log(size_seagrass), log(distance_seagrass), log(distance_mangroves) & log(size_mangroves)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$north  
  }
  else{
    formula <- n[,c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="poisson"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_sexfasciatus :  126.58813996457"

## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC abudefduf_vaigiensis :  761.404862459547"

## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC cheilio_inermis :  137.853053579635"

## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC cheilodipterus_quinquelineatus :  1484.15649033751"

## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"

## Warning: glm.fit: algorithm did not converge

## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"

## Warning: glm.fit: algorithm did not converge

## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC mulloidichthys_flavolineatus :  98.1906269028388"

## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"

## Warning: glm.fit: algorithm did not converge

## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$north"
## [1] "AIC lutjanus_fulviflamma :  37.6524153062094"

## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC parupeneus_barberinoides :  166.731713851202"

## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"

## Warning: glm.fit: algorithm did not converge

## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "AIC scolopsis_ciliata :  456.994991112409"

## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : n[, c(sp$colname)] ~ log(n$distance_seagrass) * log(n$size_seagrass) * log(n$size_mangroves) * log(n$distance_mangroves) * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)

	species	coefficient	pvalue
1	abudefduf_sexfasciatus	log(n$size_seagrass)	0.0493289
2	abudefduf_sexfasciatus	log(n$distance_mangroves)	0.0389140
3	abudefduf_sexfasciatus	n$northsouth	0.0452523
21	abudefduf_vaigiensis	log(n$distance_seagrass)	0.0000294
31	abudefduf_vaigiensis	log(n$size_seagrass)	0.0007564
4	abudefduf_vaigiensis	log(n$size_mangroves)	0.0010255
5	abudefduf_vaigiensis	log(n$distance_mangroves)	0.0009744
6	abudefduf_vaigiensis	n$mpanon-mpa	0.0005113
7	abudefduf_vaigiensis	n$depth10m	0.0000008
8	abudefduf_vaigiensis	n$northsouth	0.0012526
9	abudefduf_vaigiensis	log(n\(distance_seagrass):log(n\)size_seagrass)	0.0007965
10	abudefduf_vaigiensis	log(n\(distance_seagrass):n\)depth10m	0.0000013
11	abudefduf_vaigiensis	log(n\(size_seagrass):n\)depth10m	0.0016766
14	cheilio_inermis	n$depth10m	0.0057399
22	cheilodipterus_quinquelineatus	log(n$distance_seagrass)	0.0027203
32	cheilodipterus_quinquelineatus	log(n$size_seagrass)	0.0000000
41	cheilodipterus_quinquelineatus	log(n$size_mangroves)	0.0000000
51	cheilodipterus_quinquelineatus	log(n$distance_mangroves)	0.0000000
61	cheilodipterus_quinquelineatus	n$mpanon-mpa	0.0172170
71	cheilodipterus_quinquelineatus	n$depth10m	0.0018268
81	cheilodipterus_quinquelineatus	n$northsouth	0.0000000
91	cheilodipterus_quinquelineatus	log(n\(distance_seagrass):log(n\)size_seagrass)	0.0000000
101	cheilodipterus_quinquelineatus	log(n\(size_mangroves):n\)depth10m	0.0096215
111	cheilodipterus_quinquelineatus	log(n\(distance_mangroves):n\)depth10m	0.0490026
12	cheilodipterus_quinquelineatus	n\(mpanon-mpa:n\)depth10m	0.0050617
26	mulloidichthys_flavolineatus	log(n$distance_seagrass)	0.0377532
27	mulloidichthys_flavolineatus	log(n$distance_mangroves)	0.0131520
28	lutjanus_fulviflamma	log(n$size_seagrass)	0.0487377
29	parupeneus_barberinoides	log(n$distance_seagrass)	0.0001427
30	scolopsis_ciliata	n$depth10m	0.0005535
311	scolopsis_ciliata	log(n\(distance_seagrass):n\)depth10m	0.0084546

GLM family=Gaussian on abundance_pres

log(abundance)

glm_tab <- data.frame(species=c(), coefficient=c(), pvalue=c())

speciesrows <- c(1:3,25:28,36,39,40,42,47,52:54,58,66,84:86,88,91:100,102:104)
for (spnum in speciesrows){
  sp <- df.species_all[spnum,]
  print(sp$colname)
  n <- subset(df.sample_data, df.sample_data[c(sp$colname_pres)] > 0)
  if(nrow(n)<5){
    print("Less than 5 rows remaining in subset")
    next
  }
  if(length(unique(n$depth))==1 & length(unique(n$mpa))>1){
    formula <- log(n[,c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$north
  }
  else if (length(unique(n$depth))>1 & length(unique(n$mpa))==1){
    formula <- log(n[,c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$depth * n$north  
  }
  else if (length(unique(n$depth))==1 & length(unique(n$mpa))==1){
    formula <- log(n[,c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$north  
  }
  else{
    formula <- log(n[,c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north  
  }
  print(paste("Formula",sp$colname,":",as.character(formula)))
  res <- NULL
  tryCatch(
  res <- glm(formula, family="gaussian"),
    error=function(e){ print("GLM kon niet uitgevoerd worden.");print(geterrmessage())}
  )
  if(is.null(res)){
    next
  }
  
  coefs <- as.data.frame(coef(summary(res)))
  coefs <- subset(coefs,coefs$`Pr(>|z|)`<=0.05)
  coefs <- data.frame(species=rep(sp$colname,nrow(coefs)),coefficient=rownames(coefs),pvalue=coefs$`Pr(>|z|)`)
  coefs <- subset(coefs, coefs$coefficient != '(Intercept)')
  
  if(nrow(coefs)==0){
    next
  }
  glm_tab <- rbind(glm_tab, coefs)
  print(paste("AIC",sp$colname,": ",summary(res)$aic))
  par(mfrow=c(1,2)) 
  plot(fitted(res),residuals(res),xlab="Fitted values", ylab="Residuals", abline(h=0, lty=2))
  title(sp$colname)
  tryCatch( 
    lines(smooth.spline(fitted(res), residuals(res))), 
    error=function(e){}  )
  qqnorm(res$residuals)
  qqline(res$residuals) 
}

## [1] "abudefduf_lorenzi"
## [1] "Less than 5 rows remaining in subset"
## [1] "abudefduf_sexfasciatus"
## [1] "Formula abudefduf_sexfasciatus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "abudefduf_vaigiensis"
## [1] "Formula abudefduf_vaigiensis : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "cheilinus_chlorourus"
## [1] "Formula cheilinus_chlorourus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "cheilinus_undulatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "cheilio_inermis"
## [1] "Formula cheilio_inermis : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "cheilodipterus_quinquelineatus"
## [1] "Formula cheilodipterus_quinquelineatus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "fistularia_commersonii"
## [1] "Formula fistularia_commersonii : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "halichoeres_argus"
## [1] "Formula halichoeres_argus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "halichoeres_hortulanus"
## [1] "Formula halichoeres_hortulanus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "halichoeres_scapularis"
## [1] "Formula halichoeres_scapularis : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "lethrinus_harak"
## [1] "Less than 5 rows remaining in subset"
## [1] "lutjanus_decussatus"
## [1] "Formula lutjanus_decussatus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "lutjanus_gibbus"
## [1] "Formula lutjanus_gibbus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "lutjanus_monostigma"
## [1] "Formula lutjanus_monostigma : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "mulloidichthys_flavolineatus"
## [1] "Formula mulloidichthys_flavolineatus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinus"
## [1] "Formula parupeneus_barberinus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "siganus_guttatus"
## [1] "Formula siganus_guttatus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "siganus_virgatus"
## [1] "Formula siganus_virgatus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "sphyraena_barracuda"
## [1] "Less than 5 rows remaining in subset"
## [1] "stethojulis_trilineata"
## [1] "Formula stethojulis_trilineata : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "plectorhinchus_flavomaculatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "plectorhinchus_lineatus"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_microdon"
## [1] "Less than 5 rows remaining in subset"
## [1] "lethrinus_obsoletus"
## [1] "Formula lethrinus_obsoletus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$north"
## [1] "lutjanus_ehrenbergii"
## [1] "Formula lutjanus_ehrenbergii : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "lutjanus_fulviflamma"
## [1] "Formula lutjanus_fulviflamma : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$north"
## [1] "lutjanus_fulvus"
## [1] "Formula lutjanus_fulvus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "parupeneus_barberinoides"
## [1] "Formula parupeneus_barberinoides : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "scolopsis_bilineata"
## [1] "Formula scolopsis_bilineata : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "scolopsis_ciliata"
## [1] "Formula scolopsis_ciliata : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "scarus_psittacus"
## [1] "Formula scarus_psittacus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "epinephelus_merra"
## [1] "Formula epinephelus_merra : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$mpa * n$depth * n$north"
## [1] "siganus_spinus"
## [1] "Formula siganus_spinus : log(n[, c(sp$colname)]) ~ n$distance_seagrass * n$size_seagrass * n$depth * n$north"

knitr::kable(glm_tab, escape=TRUE)